Contacts of the helix formed by residues 61 - 73 (chain F) in PDB entry 2NPP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 61 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 3.0 12.1 + - - +
59F HIS 3.3 12.3 - - - +
60F GLY* 1.3 70.5 - - - +
62F PHE* 1.3 65.4 + - - +
63F HIS 3.2 2.7 - - - -
64F ASP* 2.7 40.8 + - + +
65F LEU* 3.2 9.1 + - - +
90F GLY* 4.2 4.5 + - - -
96F THR* 4.1 0.2 + - - -
262F ALA* 3.8 20.0 - - + +
263F PRO* 3.3 16.0 + - - +
265F TYR* 3.4 17.2 - - - -
266F CYS* 3.1 28.0 + - - -
267F TYR* 3.8 28.6 - - + +
294F ARG* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU 3.3 26.2 - - - -
18F ASN 3.8 11.7 - - - -
20F CYS* 3.4 30.7 - - + -
60F GLY 2.9 6.5 + - - -
61F GLN* 1.3 72.9 - - - +
63F HIS* 1.3 79.2 + + - +
65F LEU* 2.9 13.3 + - + +
66F MET* 2.9 56.6 + - + +
92F TYR* 3.6 26.7 - - + +
95F GLU* 3.9 20.2 - - + -
96F THR* 3.5 17.7 + - - +
99F LEU* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F CYS* 4.6 6.2 - - - +
61F GLN 3.0 3.4 + - - -
62F PHE* 1.3 95.7 - + - +
64F ASP* 1.3 53.1 + - - +
66F MET* 2.7 30.4 + - + +
67F GLU* 2.7 17.0 + - - +
70F ARG* 4.8 0.2 + - - -
92F TYR* 3.7 38.2 - + - -
292F ALA* 4.4 9.7 - - + +
294F ARG* 3.4 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 6.4 0.2 - - + -
61F GLN* 2.7 41.5 + - + +
63F HIS* 1.3 71.4 - - - +
65F LEU* 1.3 56.1 + - - +
67F GLU* 3.4 9.0 - - - +
68F LEU* 2.7 27.5 + - - +
261F SER 5.1 2.7 - - - +
262F ALA* 5.4 0.2 - - - -
263F PRO* 3.3 37.4 - - + +
267F TYR* 4.6 3.5 - - - -
289F PHE* 4.1 4.9 - - - -
291F PRO* 3.4 7.3 - - - +
292F ALA 3.2 21.8 + - - -
294F ARG* 3.9 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 4.0 21.9 - - + +
61F GLN 3.2 4.2 + - - -
62F PHE* 2.9 18.1 + - + +
64F ASP* 1.3 76.9 - - - +
66F MET* 1.3 73.9 + - + +
68F LEU* 3.0 32.1 - - + +
69F PHE* 3.1 40.0 + - + -
82F PHE* 4.1 21.3 - - + -
96F THR* 4.2 20.2 - - + +
99F LEU* 4.1 11.9 - - + -
100F LEU* 4.4 12.1 - - + -
261F SER 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ASN* 4.0 21.3 - - - +
62F PHE* 2.9 45.8 + - + +
63F HIS* 2.7 17.8 + - + +
65F LEU* 1.3 87.6 - - + +
67F GLU* 1.3 59.7 + - - +
69F PHE* 3.2 23.8 + - + +
70F ARG* 3.2 30.2 + - - +
99F LEU* 3.4 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D TRP* 3.4 20.7 + - - -
418D ARG* 2.7 31.1 + - - -
63F HIS 2.7 9.6 + - - +
64F ASP* 3.2 11.6 + - - +
66F MET* 1.3 70.1 - - - +
68F LEU* 1.3 69.9 + - - +
70F ARG* 2.7 45.9 + - - +
71F ILE* 2.9 27.6 - - + +
289F PHE* 4.1 8.4 - - + +
290F ASP* 3.8 22.6 + - - +
291F PRO 4.9 0.2 - - - -
292F ALA* 3.6 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F CYS* 4.1 16.2 - - + -
58F VAL* 5.1 3.8 - - + -
64F ASP 2.7 13.5 + - - +
65F LEU* 3.0 30.3 - - + +
67F GLU* 1.3 75.1 - - - +
69F PHE* 1.3 64.7 + - + +
71F ILE* 2.8 21.2 + - - +
72F GLY 3.0 11.3 + - - -
80F TYR* 3.9 29.6 - - + +
82F PHE* 4.6 2.7 - - + -
261F SER* 4.1 22.0 - - - +
275F ILE* 4.0 27.1 - - + +
289F PHE* 3.9 18.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D TYR* 4.8 1.2 - - - -
65F LEU* 3.1 55.0 + - + -
66F MET* 3.2 22.0 + - + +
68F LEU* 1.3 80.1 - - + +
70F ARG* 1.3 58.7 + - + +
73F GLY* 2.7 42.1 + - - +
74F LYS* 4.3 17.8 - - + +
75F SER* 4.6 9.2 - - - -
80F TYR* 3.4 42.0 - + - -
82F PHE* 4.1 14.4 - + - -
99F LEU* 4.8 4.7 - - + -
100F LEU* 4.5 2.5 - - + -
103F LEU* 4.5 16.4 - - + -
111F ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D TRP* 3.8 22.2 - - + -
418D ARG* 3.5 14.1 - - - +
456D TYR* 3.5 5.6 - - - +
457D ALA* 2.8 43.9 + - + +
66F MET* 3.2 20.3 + - - +
67F GLU* 2.7 62.3 + - - +
69F PHE* 1.3 73.8 - - + +
71F ILE* 1.3 64.8 + - + +
74F LYS* 6.2 2.2 - - - +
292F ALA* 4.2 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D TRP* 4.0 19.1 - - + +
454D HIS 4.0 2.9 - - - +
455D VAL* 3.4 22.2 - - + -
456D TYR 3.0 21.3 + - - -
459D ARG* 5.1 0.3 + - - -
67F GLU* 2.9 45.1 - - + +
68F LEU 2.8 9.5 + - - +
70F ARG* 1.3 79.7 - - + +
72F GLY* 1.3 59.2 + - - +
73F GLY 3.5 0.2 - - - -
275F ILE* 3.6 11.4 - - + -
277F GLU* 5.2 0.2 - - - +
287F LEU* 3.5 34.5 - - + +
288F GLN 5.1 1.8 - - - +
289F PHE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D TYR* 4.2 2.9 - - - -
459D ARG* 5.6 1.3 + - - -
496D LEU* 4.6 3.5 - - - +
53F THR* 4.8 3.9 + - - -
68F LEU 3.0 10.5 + - - -
71F ILE* 1.3 78.0 - - - +
73F GLY* 1.3 60.4 + - - +
78F THR* 3.3 23.0 + - - +
80F TYR* 3.3 11.4 + - - -
275F ILE* 4.0 14.1 - - - +
277F GLU* 4.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D TYR* 3.6 26.4 - - - +
459D ARG* 5.5 0.2 - - - -
69F PHE* 2.7 27.5 + - - +
71F ILE 3.5 2.6 - - - -
72F GLY* 1.3 74.7 - - - +
74F LYS* 1.3 59.1 + - - -
78F THR* 3.6 11.7 - - - -
80F TYR* 2.5 24.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il